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- PDB-6mpq: 1.95 Ang crystal structure of OXA-24/40 beta-lactamase in complex... -

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Basic information

Entry
Database: PDB / ID: 6mpq
Title1.95 Ang crystal structure of OXA-24/40 beta-lactamase in complex the inhibitor ETX2514
ComponentsBeta-lactamase
KeywordsHYDROLASE/HYDROLASE Inhibitor / beta-lactamase / inhibitor / complex / HYDROLASE / HYDROLASE-HYDROLASE Inhibitor complex
Function / homology
Function and homology information


penicillin binding / beta-lactamase activity
Similarity search - Function
Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-JXG / Beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
Authorsvan den Akker, F. / Kumar, V.
Funding support United States, 1items
OrganizationGrant numberCountry
United States
CitationJournal: MBio / Year: 2019
Title: Targeting Multidrug-ResistantAcinetobacterspp.: Sulbactam and the Diazabicyclooctenone beta-Lactamase Inhibitor ETX2514 as a Novel Therapeutic Agent.
Authors: Barnes, M.D. / Kumar, V. / Bethel, C.R. / Moussa, S.H. / O'Donnell, J. / Rutter, J.D. / Good, C.E. / Hujer, K.M. / Hujer, A.M. / Marshall, S.H. / Kreiswirth, B.N. / Richter, S.S. / Rather, P. ...Authors: Barnes, M.D. / Kumar, V. / Bethel, C.R. / Moussa, S.H. / O'Donnell, J. / Rutter, J.D. / Good, C.E. / Hujer, K.M. / Hujer, A.M. / Marshall, S.H. / Kreiswirth, B.N. / Richter, S.S. / Rather, P.N. / Jacobs, M.R. / Papp-Wallace, K.M. / van den Akker, F. / Bonomo, R.A.
History
DepositionOct 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0493
Polymers27,7341
Non-polymers3152
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.562, 102.562, 87.005
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-570-

HOH

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Components

#1: Protein Beta-lactamase / / Beta-lactamase OXA-33 / Betalactamase OXA24 / Carbapenem-hydrolyzing beta-lactamase OXA-40 / ...Beta-lactamase OXA-33 / Betalactamase OXA24 / Carbapenem-hydrolyzing beta-lactamase OXA-40 / Carbapenem-hydrolyzing oxacillinase / Carbapenem-hydrolyzing oxacillinase OXA-40 / Carbapenemase OXA-24 / Class D beta-lactamase OXA-40 / OXA24 B-lactamase / Oxa40


Mass: 27733.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: blaOXA-33, bla-OXA-40, blaOXA-24, blaOXA-40, oxa-24, oxa40
Production host: Escherichia coli (E. coli) / References: UniProt: Q8RLA6
#2: Chemical ChemComp-JXG / (2S,5R)-1-formyl-3-methyl-5-[(sulfooxy)amino]-1,2,5,6-tetrahydropyridine-2-carboxamide / ETX2514 bound form


Mass: 279.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13N3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.12 Å3/Da / Density % sol: 70.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: of 0.1 M HEPES sodium salt pH 7.5, 10% (v/v) isopropanol and 20% (w/v) PEG 4000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.95→72.52 Å / Num. obs: 34248 / % possible obs: 99.6 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.043 / Rrim(I) all: 0.114 / Net I/σ(I): 11.3
Reflection shellResolution: 1.95→2 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.791 / Num. unique obs: 2350 / CC1/2: 0.767 / Rpim(I) all: 0.337 / Rrim(I) all: 0.863 / % possible all: 99.3

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.31data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.24data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3mbz

3mbz


Resolution: 1.95→37.5 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.955 / SU B: 4.079 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.108
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2097 1735 5.1 %RANDOM
Rwork0.1865 ---
obs0.1877 32479 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 110.79 Å2 / Biso mean: 32.085 Å2 / Biso min: 17.79 Å2
Baniso -1Baniso -2Baniso -3
1--2.25 Å20 Å20 Å2
2---2.25 Å20 Å2
3---4.5 Å2
Refinement stepCycle: final / Resolution: 1.95→37.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1950 0 19 174 2143
Biso mean--37.5 38.97 -
Num. residues----245
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192046
X-RAY DIFFRACTIONr_bond_other_d0.0020.022002
X-RAY DIFFRACTIONr_angle_refined_deg1.5051.9652765
X-RAY DIFFRACTIONr_angle_other_deg1.1773.0014619
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2755254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.35325.55690
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.27115380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.581157
X-RAY DIFFRACTIONr_chiral_restr0.1170.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022299
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02460
LS refinement shellResolution: 1.95→2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 121 -
Rwork0.316 2346 -
all-2467 -
obs--99.04 %

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